Out-of-universe, according to some recent reports, there was some sort of problem between Gates McFadden and producer/writer Maurice Hurley. I've heard this characterized in some places as sexual harassment, but I'm not sure that's based on any actual allegations. Rick Berman did say he was at the center of it, though:
Gates McFadden fired at end of first season because head writer Maurice Hurley "he had a real bone to pick" with Gates and din’t [sic] like her acting, Berman brought Gates back for 3rd season after Hurley left
(Det citatet är från sammanfattningen här .)